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Nowadays, food treatment technologies are constantly evolving due to an increasing demand for healthier and tastier food with longer shelf lives. In this review, our aim is to highlight the advantages and disadvantages of some of the most exploited industrial techniques for food processing and microorganism deactivation, dividing them into those that exploit high temperatures (pasteurization, sterilization, aseptic packaging) and those that operate thanks to their inherent chemical–physical principles (ultrasound, ultraviolet radiation, ozonation, high hydrostatic pressure). The traditional thermal methods can reduce the number of pathogenic microorganisms to safe levels, but non-thermal technologies can also reduce or remove the adverse effects that occur using high temperatures. In the case of ultrasound, which inactivates pathogens, recent advances in food treatment are reported. Throughout the text, novel discoveries of the last decade are presented, and non-thermal methods have been demonstrated to be more attractive for processing a huge variety of foods. Preserving the quality and nutritional values of the product itself and at the same time reducing bacteria and extending shelf life are the primary targets of conscious producers, and with non-thermal technologies, they are increasingly possible.